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<title>Adapter Content</title>
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<h1>Adapter Content</h1>
<h2>Summary</h2>
<p>
The Kmer Content module will do a generic analysis of all of the Kmers
in your library to find those which do not have even coverage through 
the length of your reads.  This can find a number of different sources
of bias in the library which can include the presence of read-through
adapter sequences building up on the end of your sequences.
</p>
<p>
You can however find that the presence of any overrepresented sequences
in your library (such as adapter dimers) will cause the Kmer plot to
be dominated by the Kmers these sequences contain, and that it's not
always easy to see if there are other biases present in which you might
be interested.
</p>
<p>
One obvious class of sequences which you might want to analyse are 
adapter sequences.  It is useful to know if your library contains a 
significant amount of adapter in order to be able to assess whether 
you need to adapter trim or not.  Although the Kmer analysis can 
theoretically spot this kind of contamination it isn't always clear.
This module therefore does a specific search for a set of separately
defined Kmers and will give you a view of the total proportion of your
library which contain these Kmers.  A results trace will always be 
generated for all of the sequences present in the adapter config file 
so you can see the adapter content of your library, even if it's low.
</p>
<p>
The plot itself shows a cumulative percentage count of the proportion
of your library which has seen each of the adapter sequences at each
position.  Once a sequence has been seen in a read it is counted as
being present right through to the end of the read so the percentages
you see will only increase as the read length goes on.
</p>

<h2>Warning</h2>
<p>
This module will issue a warning if any sequence is present in more
than 5% of all reads.
</p>

<h2>Failure</h2>
<p>
This module will issue a warning if any sequence is present in more
than 10% of all reads.
</p>

<h2>Common reasons for warnings</h2>
<p>
Any library where a reasonable proportion of the insert sizes are shorter
than the read length will trigger this module.  This doesn't indicate a 
problem as such - just that the sequences will need to be adapter trimmed
before proceeding with any downstream analysis.
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